Naslov
From DNA Sequences to Chemical Structures – Methods for Mining Microbial Genomic and Metagenomic Datasets for New Natural Products

Autori
Žučko, Jurica ; Starčević, Antonio ; Diminić, Janko ; Elbekali, Mouhsine ; Lisfi, Mohamed ; Long, Paul F. ; Cullum, John ; Hranueli, Daslav

Izvornik
Food technology and biotechnology (1330-9862) 48 (2010), 2; 234-242

Vrsta, podvrsta i kategorija rada
Radovi u časopisima, članak, znanstveni

Ključne riječi
polyketides; non-ribosomal peptides; Actinobacteria; homologous recombination

Sažetak
Rapid mining of large genomic and metagenomic data sets for modular polyketide synthases, non-ribosomal peptide synthetases and hybrid polyketide synthases/non-ribosomal peptide synthetases biosynthetic gene clusters was achieved using the generic computer program packages ClustScan and CompGen. These program packages perform the annotation with the hierarchical structuring into polypeptides, modules and domains, as well as storage and graphical presentations of the data. This aims to achieve the most accurate predictions of the activities and specificities of catalytically active domains that can be made with present knowledge, leading to a prediction of the most likely chemical structures produced by these enzymes. The program packages also allow generation of novel clusters by homologous recombination of the annotated genes in silico. ClustScan and CompGen were used to construct a custom database of known compounds (CSDB) and of predicted entirely novel recombinant products (r-CSDB), that can be used for in silico screening with computer aided drug design technology. The use of these programs have been exemplified by analysing genomic sequences from terrestrial prokaryotes and eukaryotic microorganisms, a marine metagenomic dataset and a newly discovered example of a "shared metabolic pathway" in marine-microbial endosymbiosis.

Izvorni jezik
Engleski

Znanstvena područja
Biotehnologija

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